@article {pmid40335465,
year = {2025},
author = {Romano, S and Wirbel, J and Ansorge, R and Schudoma, C and Ducarmon, QR and Narbad, A and Zeller, G},
title = {Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4227},
pmid = {40335465},
issn = {2041-1723},
support = {BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; SEG 9093//European Molecular Biology Organization (EMBO)/ ; EMBO ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; 395357507 - SFB 1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Parkinson Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Machine Learning ; Metagenome ; },
abstract = {There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (4489 samples). Within most studies, microbiome-based machine learning models accurately classify PD patients (average AUC 71.9%). However, these models are study-specific and do not generalise well across other studies (average AUC 61%). Training models on multiple datasets improves their generalizability (average LOSO AUC 68%) and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Moreover, meta-analysis of shotgun metagenomes delineates PD-associated microbial pathways potentially contributing to gut health deterioration and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, microbial pathways for solvent and pesticide biotransformation are enriched in PD. These results align with epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbes modulate their toxicity. Here, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.},
}

*Parkinson Disease/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
Humans
*Machine Learning
Metagenome

@article {pmid40335388,
year = {2025},
author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R},
title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.004},
pmid = {40335388},
issn = {1878-4372},
abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.},
}

@article {pmid40333159,
year = {2025},
author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F},
title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333159},
issn = {2076-0817},
support = {22LCYY-QH10//Jinling Hospital/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; *Psoriasis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.},
}

Humans
*Dysbiosis/microbiology/therapy
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Probiotics/administration & dosage
*Psoriasis/microbiology/therapy
RNA, Ribosomal, 16S/genetics

@article {pmid40333054,
year = {2025},
author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and da Silva, MS and Weber, MN and de Barros, MP and Spilki, FR},
title = {Virome of Terrestrial Mammals and Bats from Southern Brazil: Circulation of New Putative Members of the Togaviridae Family and Other Findings.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333054},
issn = {2076-0817},
support = {405786/2022-0//CNPQ/ ; },
mesh = {Animals ; Brazil/epidemiology ; *Chiroptera/virology ; *Virome ; *Mammals/virology ; Phylogeny ; Metagenomics ; Humans ; },
abstract = {The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic sequencing. Akodon montensis (n = 15 individuals) and Coendou spinosus (n = 4) harbored Chikungunya virus (ChikV, Togaviridae), marking its first detection in these hosts. Molossus molossus (n = 17) presented Coronaviridae and Orthoherpesviridae, while Eptesicus furinalis (n = 1) also carried Coronaviridae. A broad virome diversity, including Togaviridae and Adenoviridae members, was identified in Didelphis albiventris (n = 43), with significant relevance to human health. Additional species, such as Callithrix jacchus (n = 1), Leopardus guttulus (n = 1), Myocastor coypus (n = 1), Monodelphis iheringi (n = 1), Thaptomys nigrita (n = 1), Sooretamys angouya (n = 1), Brucepattersonius iheringi (n = 1), and Lasiurus blossevillii (n = 1), contributed to insights into viral reservoirs. These results underscore the importance of virome studies in regions harboring high biodiversity, emphasizing genomic surveillance as a vital tool for monitoring zoonotic viruses and safeguarding global health.},
}

Animals
Brazil/epidemiology
*Chiroptera/virology
*Virome
*Mammals/virology
Phylogeny
Metagenomics
Humans

@article {pmid40330019,
year = {2025},
author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S},
title = {Investigation of dynamic microbial migration patterns in the respiratory tract.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542562},
pmid = {40330019},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.

METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.

RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.

CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.},
}

Humans
*Respiratory Tract Infections/microbiology
Prospective Studies
Male
Female
Middle Aged
*Microbiota
Sputum/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Respiratory System/microbiology
Adult
High-Throughput Nucleotide Sequencing
Metagenomics
Oropharynx/microbiology
Bayes Theorem
*Bacteria/classification/genetics/isolation & purification

@article {pmid40329426,
year = {2025},
author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M},
title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {115},
pmid = {40329426},
issn = {2049-2618},
support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; Female ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Male ; Adult ; Metagenomics/methods ; *Oropharynx/microbiology ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Family Characteristics ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.

RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.

CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.},
}

Humans
*Microbiota/genetics
Female
*Bacteria/genetics/classification/isolation & purification/drug effects
Male
Adult
Metagenomics/methods
*Oropharynx/microbiology
Middle Aged
*Drug Resistance, Microbial/genetics
Family Characteristics
Young Adult
Metagenome

@article {pmid40329425,
year = {2025},
author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M},
title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {48},
pmid = {40329425},
issn = {2524-6372},
support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.

RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.

CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.},
}

@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}

*Snow/microbiology
Gammaproteobacteria/metabolism/genetics/classification
Metagenomics/methods
Metagenome
*Seawater/microbiology
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
Phytoplankton/microbiology/metabolism
Multiomics

@article {pmid40328944,
year = {2025},
author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE},
title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1184-1197},
pmid = {40328944},
issn = {2058-5276},
support = {R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK121822//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Feces/microbiology ; Female ; *Metagenomics/methods ; Bayes Theorem ; Longitudinal Studies ; Escherichia coli/genetics/isolation & purification/classification ; Infant ; Algorithms ; Enterococcus faecalis/genetics/isolation & purification/classification ; Adult ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.},
}

Humans
*Microbiota/genetics
Feces/microbiology
Female
*Metagenomics/methods
Bayes Theorem
Longitudinal Studies
Escherichia coli/genetics/isolation & purification/classification
Infant
Algorithms
Enterococcus faecalis/genetics/isolation & purification/classification
Adult
*Bacteria/genetics/classification/isolation & purification

@article {pmid40328731,
year = {2025},
author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y},
title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4211},
pmid = {40328731},
issn = {2041-1723},
support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Insulin Resistance/physiology ; Female ; *Bile Acids and Salts/metabolism ; Blood Glucose/metabolism ; Postprandial Period ; Insulin/blood/metabolism ; Double-Blind Method ; Aged ; *Dietary Fats, Unsaturated/administration & dosage ; Feces/microbiology/chemistry ; Adult ; Prediabetic State/metabolism/diet therapy/microbiology ; },
abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.},
}

Humans
*Gastrointestinal Microbiome/physiology
Middle Aged
Male
*Insulin Resistance/physiology
Female
*Bile Acids and Salts/metabolism
Blood Glucose/metabolism
Postprandial Period
Insulin/blood/metabolism
Double-Blind Method
Aged
*Dietary Fats, Unsaturated/administration & dosage
Feces/microbiology/chemistry
Adult
Prediabetic State/metabolism/diet therapy/microbiology

@article {pmid40325616,
year = {2025},
author = {Xu, HY and Jiang, MT and Yang, YF and Huang, Y and Yang, WD and Li, HY and Wang, X},
title = {Microalgae-Based Fucoxanthin Attenuates Rheumatoid Arthritis by Targeting the JAK-STAT Signaling Pathway and Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {19},
pages = {11708-11719},
doi = {10.1021/acs.jafc.4c12474},
pmid = {40325616},
issn = {1520-5118},
mesh = {*Xanthophylls/administration & dosage ; *Arthritis, Rheumatoid/drug therapy/microbiology/genetics/metabolism/immunology ; *Gastrointestinal Microbiome/drug effects ; Humans ; Signal Transduction/drug effects ; Animals ; *Microalgae/chemistry ; Mice ; Male ; *Janus Kinases/genetics/metabolism/immunology ; *STAT Transcription Factors/genetics/metabolism/immunology ; *Diatoms/chemistry ; },
abstract = {Fucoxanthin, an abundant carotenoid in marine algae, has garnered attention for its diverse health benefits, including anti-inflammatory and anticancer properties. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation and damage. This study investigated the therapeutic potential of fucoxanthin extracted from Phaeodactylum tricornutum in collagen-induced RA. Our results demonstrated that fucoxanthin significantly alleviated RA symptoms, including weight loss, joint swelling, and decreased appetite. Histological analysis revealed that fucoxanthin mitigated synovial inflammation, cartilage damage, and bone erosion. Mechanistically, transcriptomic analysis and cell experiments indicated that fucoxanthin suppressed the JAK-STAT signaling pathway by downregulating the expression of inflammatory cytokines, such as IL-6 and IL-1β. Furthermore, metagenomic analysis suggested that fucoxanthin restored the altered gut microbiota composition associated with RA. These findings highlight the therapeutic potential of fucoxanthin from P. tricornutum in the management of RA by targeting multiple pathways, including inflammation and gut microbiota.},
}

*Xanthophylls/administration & dosage
*Arthritis, Rheumatoid/drug therapy/microbiology/genetics/metabolism/immunology
*Gastrointestinal Microbiome/drug effects
Humans
Signal Transduction/drug effects
Animals
*Microalgae/chemistry
Mice
Male
*Janus Kinases/genetics/metabolism/immunology
*STAT Transcription Factors/genetics/metabolism/immunology
*Diatoms/chemistry

@article {pmid40250281,
year = {2025},
author = {Chen, Y and Hu, S and Hu, B and Li, Y and Chen, Z},
title = {Functional insights into microbial community dynamics and resilience in mycorrhizal associated constructed wetlands under pesticide stress.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138315},
doi = {10.1016/j.jhazmat.2025.138315},
pmid = {40250281},
issn = {1873-3336},
mesh = {*Wetlands ; *Mycorrhizae/drug effects/genetics/physiology ; *Pesticides/toxicity ; *Microbiota/drug effects ; Soil Microbiology ; Stress, Physiological ; Bacteria/genetics ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are critical mutualistic symbionts in most terrestrial ecosystems, where they facilitate nutrient acquisition, enhance plant resilience to environmental stressors, and shape the surrounding microbiome. However, its contributions (especially for microorganisms) to constructed wetlands (CWs) under pesticide stress remain poorly understood. This study investigated the effects of AMF on microbial community composition, diversity, metabolic pathways, and functional genes by metagenomics in CWs exposed to pesticides stress. Using comparative analyses of AMF-colonized and non-colonized CWs, we found that AMF enhanced overall microbial diversity, as evidenced by increases of 2.22 % (Chao1) and 2.83 % (observed species). Under fungicide stress, nitrogen-cycling microorganisms (e.g., Nitrososphaerota and Mucoromycota) increased in relative abundance, while carbon cycle-related microorganisms (e.g., Pseudomonadota and Bacteroidota) generally declined. AMF colonization improved microbial resilience, demonstrated by a 312 % rise in Rhizophagus abundance and significant increases in phosphorus-cycling microorganisms (e.g., Bradyrhizobium and Mesorhizobium). Functional gene analysis further revealed that AMF helped mitigate fungicide-induced reductions in genes related to nitrogen and carbon cycling, lowering the average decline rates to 4.02 % and 1.44 %, respectively, compared to higher rates in non-AMF treatments. In summary, these findings highlight the crucial role of AMF in enhancing pesticide stress resilience, maintaining microbial community stability, and improving the bioremediation capacity of CWs.},
}

*Wetlands
*Mycorrhizae/drug effects/genetics/physiology
*Pesticides/toxicity
*Microbiota/drug effects
Soil Microbiology
Stress, Physiological
Bacteria/genetics

@article {pmid40250268,
year = {2025},
author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC},
title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138285},
doi = {10.1016/j.jhazmat.2025.138285},
pmid = {40250268},
issn = {1873-3336},
mesh = {*Quorum Sensing ; Homeostasis ; *Ammonium Compounds/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; Nitrogen/metabolism ; 4-Butyrolactone/analogs & derivatives/pharmacology ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Anaerobiosis ; },
abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.},
}

*Quorum Sensing
Homeostasis
*Ammonium Compounds/metabolism
*Microbial Consortia
Oxidation-Reduction
Nitrogen/metabolism
4-Butyrolactone/analogs & derivatives/pharmacology
Bioreactors/microbiology
Bacteria/metabolism/genetics
Anaerobiosis

@article {pmid40207938,
year = {2025},
author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ},
title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.},
journal = {mBio},
volume = {16},
number = {5},
pages = {e0069925},
doi = {10.1128/mbio.00699-25},
pmid = {40207938},
issn = {2150-7511},
support = {FRN-142349//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Eukaryota/genetics ; *Computational Biology/methods ; *Blastocystis/genetics ; Gastrointestinal Microbiome/genetics ; Metagenome ; Whole Genome Sequencing ; Software ; },
abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.},
}

*Metagenomics/methods
Humans
*Eukaryota/genetics
*Computational Biology/methods
*Blastocystis/genetics
Gastrointestinal Microbiome/genetics
Metagenome
Whole Genome Sequencing
Software

@article {pmid40188549,
year = {2025},
author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F},
title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138164},
doi = {10.1016/j.jhazmat.2025.138164},
pmid = {40188549},
issn = {1873-3336},
mesh = {*Zinc Oxide/toxicity ; *Microplastics/toxicity ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil Pollutants/toxicity ; Metagenomics ; *Nanoparticles/toxicity ; Bacteria/drug effects/genetics ; Agriculture ; Fungi/drug effects/genetics ; Soil/chemistry ; *Metal Nanoparticles/toxicity ; },
abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.},
}

*Zinc Oxide/toxicity
*Microplastics/toxicity
*Soil Microbiology
*Microbiota/drug effects
*Soil Pollutants/toxicity
Metagenomics
*Nanoparticles/toxicity
Bacteria/drug effects/genetics
Agriculture
Fungi/drug effects/genetics
Soil/chemistry
*Metal Nanoparticles/toxicity

@article {pmid40168930,
year = {2025},
author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY},
title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138077},
doi = {10.1016/j.jhazmat.2025.138077},
pmid = {40168930},
issn = {1873-3336},
mesh = {*Rhizosphere ; *Lactuca/genetics/microbiology/metabolism ; Genotype ; *Soil Pollutants/metabolism ; *Bacteria/genetics/metabolism ; Soil Microbiology ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology/metabolism ; *Diethylhexyl Phthalate/metabolism ; *Phthalic Acids/metabolism ; Microbiota ; },
abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.},
}

*Rhizosphere
*Lactuca/genetics/microbiology/metabolism
Genotype
*Soil Pollutants/metabolism
*Bacteria/genetics/metabolism
Soil Microbiology
Biodegradation, Environmental
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology/metabolism
*Diethylhexyl Phthalate/metabolism
*Phthalic Acids/metabolism
Microbiota

@article {pmid40131312,
year = {2025},
author = {Herazo-Álvarez, J and Mora, M and Cuadros-Orellana, S and Vilches-Ponce, K and Hernández-García, R},
title = {A review of neural networks for metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
pmid = {40131312},
issn = {1477-4054},
support = {2022-21221825//National Agency for Research and Development/ ; EQM210185//Fondequip/ ; },
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Metagenome ; Humans ; Microbiota ; Machine Learning ; Deep Learning ; },
abstract = {One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.},
}

*Metagenomics/methods
*Neural Networks, Computer
*Metagenome
Humans
Microbiota
Machine Learning
Deep Learning

@article {pmid40086246,
year = {2025},
author = {Han, NN and Yang, JH and Wu, GG and Yang, JH and Jin, JA and Fan, NS and Jin, RC},
title = {Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {137886},
doi = {10.1016/j.jhazmat.2025.137886},
pmid = {40086246},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Sulfamethazine/pharmacology ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Oxidation-Reduction ; *Ammonia/metabolism ; Anaerobiosis ; Pseudomonas/genetics/drug effects/metabolism ; *Microbial Consortia ; },
abstract = {Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.},
}

*Anti-Bacterial Agents/pharmacology
*Sulfamethazine/pharmacology
Sewage/microbiology
*Drug Resistance, Microbial/genetics
Oxidation-Reduction
*Ammonia/metabolism
Anaerobiosis
Pseudomonas/genetics/drug effects/metabolism
*Microbial Consortia

@article {pmid40318372,
year = {2025},
author = {Chu, D and Zhang, H and Wang, Z and Ning, K},
title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179522},
doi = {10.1016/j.scitotenv.2025.179522},
pmid = {40318372},
issn = {1879-1026},
mesh = {*Ecosystem ; *Fresh Water/microbiology ; China ; *Water Microbiology ; *Microbiota ; Bacteria ; Metagenome ; Lakes/microbiology ; *Environmental Monitoring ; },
abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.},
}

*Ecosystem
*Fresh Water/microbiology
China
*Water Microbiology
*Microbiota
Bacteria
Metagenome
Lakes/microbiology
*Environmental Monitoring

@article {pmid40315414,
year = {2025},
author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ},
title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012268},
pmid = {40315414},
issn = {1553-7358},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; *Viruses/genetics/classification ; Computational Biology/methods ; Feces/virology ; Metagenome/genetics ; Infant ; Databases, Genetic ; },
abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome/genetics
*Viruses/genetics/classification
Computational Biology/methods
Feces/virology
Metagenome/genetics
Infant
Databases, Genetic

@article {pmid40252413,
year = {2025},
author = {Okamura, T and Hasegawa, Y and Ohno, Y and Saijo, Y and Nakanishi, N and Honda, A and Hamaguchi, M and Takano, H and Fukui, M},
title = {Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet.},
journal = {Chemosphere},
volume = {379},
number = {},
pages = {144401},
doi = {10.1016/j.chemosphere.2025.144401},
pmid = {40252413},
issn = {1879-1298},
mesh = {Animals ; *Food Hypersensitivity/immunology ; *Diet, High-Fat/adverse effects ; Mice ; Mice, Inbred BALB C ; Gastrointestinal Microbiome/drug effects ; Ovalbumin/immunology ; Immunoglobulin E/blood ; *Microplastics/toxicity ; Administration, Oral ; *Polystyrenes/toxicity ; Female ; },
abstract = {The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.},
}

Animals
*Food Hypersensitivity/immunology
*Diet, High-Fat/adverse effects
Mice
Mice, Inbred BALB C
Gastrointestinal Microbiome/drug effects
Ovalbumin/immunology
Immunoglobulin E/blood
*Microplastics/toxicity
Administration, Oral
*Polystyrenes/toxicity
Female

@article {pmid40252261,
year = {2025},
author = {Li, B and Liang, C and Xu, B and Song, P and Liu, D and Zhang, J and Gu, H and Jiang, F and Gao, H and Cai, Z and Zhang, T},
title = {Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer.},
journal = {Microbiological research},
volume = {297},
number = {},
pages = {128182},
doi = {10.1016/j.micres.2025.128182},
pmid = {40252261},
issn = {1618-0623},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Deer/microbiology/metabolism ; *Seasons ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Tibet ; Feces/microbiology ; Metabolomics ; Phylogeny ; },
abstract = {Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Deer/microbiology/metabolism
*Seasons
*Metabolome
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics
Fatty Acids, Volatile/metabolism
Tibet
Feces/microbiology
Metabolomics
Phylogeny

@article {pmid40172536,
year = {2025},
author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR},
title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.},
journal = {Infection and immunity},
volume = {93},
number = {5},
pages = {e0056924},
doi = {10.1128/iai.00569-24},
pmid = {40172536},
issn = {1098-5522},
support = {IOS-2131060//National Science Foundation/ ; IOS-2131061//National Science Foundation/ ; BB/W013517/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Skin/microbiology/immunology ; *Xenopus laevis/microbiology/immunology/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Batrachochytrium ; Transcriptome ; },
abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Skin/microbiology/immunology
*Xenopus laevis/microbiology/immunology/genetics
*Microbiota/drug effects
RNA, Ribosomal, 16S/genetics
Batrachochytrium
Transcriptome

@article {pmid39543873,
year = {2025},
author = {Saraswat, I and Goel, A},
title = {Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions.},
journal = {Current pharmaceutical biotechnology},
volume = {26},
number = {5},
pages = {680-699},
pmid = {39543873},
issn = {1873-4316},
mesh = {Humans ; *Neoplasms/microbiology/therapy/immunology ; Probiotics/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Microbiota/drug effects ; },
abstract = {Cancer is a predominant cause of mortality worldwide, necessitating the development of innovative therapeutic techniques. The human microbiome, particularly the gut microbiota, has become a significant element in cancer research owing to its essential role in sustaining health and influencing disease progression. This review examines the microbiome's makeup and essential functions, including immunological modulation and metabolic regulation, which may be evaluated using sophisticated methodologies such as metagenomics and 16S rRNA sequencing. The microbiome influences cancer development by promoting inflammation, modulating the immune system, and producing carcinogenic compounds. Dysbiosis, or microbial imbalance, can undermine the epithelial barrier and facilitate cancer. The microbiome influences chemotherapy and radiation results by modifying drug metabolism, either enhancing or reducing therapeutic efficacy and contributing to side effects and toxicity. Comprehending these intricate relationships emphasises the microbiome's significance in oncology and accentuates the possibility for microbiome-targeted therapeutics. Contemporary therapeutic approaches encompass the utilisation of probiotics and dietary components to regulate the microbiome, enhance treatment efficacy, and minimise unwanted effects. Advancements in research indicate that personalised microbiome-based interventions, have the potential to transform cancer therapy, by providing more effective and customised treatment alternatives. This study aims to provide a comprehensive analysis of the microbiome's influence on the onset and treatment of cancer, while emphasising current trends and future possibilities for therapeutic intervention.},
}

Humans
*Neoplasms/microbiology/therapy/immunology
Probiotics/therapeutic use
*Gastrointestinal Microbiome/drug effects
Animals
*Microbiota/drug effects

@article {pmid40244062,
year = {2025},
author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC},
title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40244062},
issn = {1751-7370},
support = {COEVOPRO 802242//European Research Council Starting/ ; 802242//European Research Council Starting Grant/ ; //EPA Cephalosporin Junior Research Fellowship at Linacre College/ ; },
mesh = {Animals ; *Evolution, Molecular ; *Dysbiosis/microbiology ; *Microbiota ; *Staphylococcus aureus/genetics/pathogenicity/physiology ; Virulence ; Whole Genome Sequencing ; *Host-Pathogen Interactions ; Biofilms/growth & development ; Caenorhabditis elegans/microbiology ; },
abstract = {Pathogens newly invading a host must compete with resident microbiota. This within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a natural microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.},
}

Animals
*Evolution, Molecular
*Dysbiosis/microbiology
*Microbiota
*Staphylococcus aureus/genetics/pathogenicity/physiology
Virulence
Whole Genome Sequencing
*Host-Pathogen Interactions
Biofilms/growth & development
Caenorhabditis elegans/microbiology

@article {pmid40189243,
year = {2025},
author = {Chitcharoen, S and Sawaswong, V and Klomkliew, P and Chanchaem, P and Payungporn, S},
title = {Comparative analysis of human gut bacterial microbiota between shallow shotgun metagenomic sequencing and full-length 16S rDNA amplicon sequencing.},
journal = {Bioscience trends},
volume = {19},
number = {2},
pages = {232-242},
doi = {10.5582/bst.2024.01393},
pmid = {40189243},
issn = {1881-7823},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/classification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; },
abstract = {The human gut microbiome is increasingly recognized as important to health and disease, influencing immune function, metabolism, mental health, and chronic illnesses. Two widely used, cost-effective, and fast approaches for analyzing gut microbial communities are shallow shotgun metagenomic sequencing (SSMS) and full-length 16S rDNA sequencing. This study compares these methods across 43 stool samples, revealing notable differences in taxonomic and species-level detection. At the genus level, Bacteroides was most abundant in both methods, with Faecalibacterium showing similar trends but Prevotella was more abundant in full-length 16S rDNA. Genera such as Alistipes and Akkermansia were more frequently detected by full-length 16S rDNA, whereas Eubacterium and Roseburia were more prevalent in SSMS. At the species level, Faecalibacterium prausnitzii, a key indicator of gut health, was abundant across both datasets, while Bacteroides vulgatus was more frequently detected by SSMS. Species within Parabacteroides and Bacteroides were primarily detected by 16S rDNA, contrasting with higher SSMS detection of Prevotella copri and Oscillibacter valericigenes. LEfSe analysis identified 18 species (9 species in each method) with significantly different detection between methods, underscoring the impact of methodological choice on microbial diversity and abundance. Differences in classification databases, such as Ribosomal Database Project (RDP) for 16S rDNA and Kraken2 for SSMS, further highlight the influence of database selection on outcomes. These findings emphasize the importance of carefully selecting sequencing methods and bioinformatics tools in microbiome research, as each approach demonstrates unique strengths and limitations in capturing microbial diversity and relative abundances.},
}

Humans
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Feces/microbiology
*Bacteria/genetics/classification
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
Metagenome
Sequence Analysis, DNA/methods

@article {pmid40116459,
year = {2025},
author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M},
title = {Dietary protein source alters gut microbiota composition and function.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf048},
pmid = {40116459},
issn = {1751-7370},
support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; 7002782//USDA National Institute of Food and Agriculture/ ; P30 DK034987/NH/NIH HHS/United States ; },
mesh = {Animals ; *Dietary Proteins/metabolism/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Bacteria/classification/genetics ; Mice, Inbred C57BL ; Proteomics ; Diet ; Male ; Amino Acids/metabolism ; },
abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.},
}

Animals
*Dietary Proteins/metabolism/administration & dosage
Mice
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Bacteria/classification/genetics
Mice, Inbred C57BL
Proteomics
Diet
Male
Amino Acids/metabolism

@article {pmid40327160,
year = {2025},
author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z},
title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {282},
pmid = {40327160},
issn = {1432-0991},
support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal & Child Research Fund Project" of Biostime Institute of Nutrition & Care/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice
*Osteopontin/genetics/metabolism
Mice, Knockout
Lipid Metabolism/genetics
*Intestines/microbiology
Mice, Inbred C57BL
Transcriptome
Bacteria/classification/genetics/isolation & purification

@article {pmid40325896,
year = {2025},
author = {Ikegwuoha, NPP and Hanekom, T and Booysen, E and Jason, C and Parker-Nance, S and Davies-Coleman, MT and van Zyl, LJ and Trindade, M},
title = {Fimsbactin Siderophores From a South African Marine Sponge Symbiont, Marinomonas sp. PE14-40.},
journal = {Microbial biotechnology},
volume = {18},
number = {5},
pages = {e70155},
pmid = {40325896},
issn = {1751-7915},
support = {//South African Medical Research Council (Self-Initiated grant)/ ; 87326//DSI/NRF SARChI research chair in Microbial Genomics/ ; 312184//European Union PharmaSea Consortium/ ; 129660//National Research Foundation/ ; },
mesh = {*Siderophores/chemistry/metabolism/genetics/isolation & purification ; Multigene Family ; Animals ; Biosynthetic Pathways/genetics ; *Porifera/microbiology ; Symbiosis ; Hydroxamic Acids/metabolism/chemistry ; },
abstract = {Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1-6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.},
}

*Siderophores/chemistry/metabolism/genetics/isolation & purification
Multigene Family
Animals
Biosynthetic Pathways/genetics
*Porifera/microbiology
Symbiosis
Hydroxamic Acids/metabolism/chemistry

@article {pmid40302016,
year = {2025},
author = {Zhou, H and Tang, L and Fenton, KA and Song, X},
title = {Exploring and evaluating microbiome resilience in the gut.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {5},
pages = {},
doi = {10.1093/femsec/fiaf046},
pmid = {40302016},
issn = {1574-6941},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Host Microbial Interactions ; Bacteria/genetics/classification ; Probiotics ; *Gastrointestinal Tract/microbiology ; Animals ; },
abstract = {The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.},
}

*Gastrointestinal Microbiome/physiology
Humans
Host Microbial Interactions
Bacteria/genetics/classification
Probiotics
*Gastrointestinal Tract/microbiology
Animals

@article {pmid40220806,
year = {2025},
author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q},
title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.},
journal = {International journal of biological macromolecules},
volume = {309},
number = {Pt 3},
pages = {142983},
doi = {10.1016/j.ijbiomac.2025.142983},
pmid = {40220806},
issn = {1879-0003},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Rats ; *Polystyrenes/toxicity ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics/drug effects ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Humans ; *Genes, Bacterial ; Male ; *Drug Resistance, Bacterial/genetics/drug effects ; Bacteria/genetics/drug effects ; },
abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
Rats
*Polystyrenes/toxicity
*Microplastics/toxicity
*Drug Resistance, Microbial/genetics/drug effects
Metagenomics
Anti-Bacterial Agents/pharmacology
Humans
*Genes, Bacterial
Male
*Drug Resistance, Bacterial/genetics/drug effects
Bacteria/genetics/drug effects

@article {pmid40053318,
year = {2025},
author = {Nihalani, R and Zola, J and Aluru, S},
title = {Disambiguating a Soft Metagenomic Clustering.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {32},
number = {5},
pages = {473-485},
doi = {10.1089/cmb.2024.0825},
pmid = {40053318},
issn = {1557-8666},
mesh = {*Metagenomics/methods ; Animals ; Cluster Analysis ; Rats ; Algorithms ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; },
abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.},
}

*Metagenomics/methods
Animals
Cluster Analysis
Rats
Algorithms
RNA, Ribosomal, 16S/genetics
Metagenome
Computational Biology/methods
Sequence Analysis, DNA/methods
Gastrointestinal Microbiome/genetics

@article {pmid40043973,
year = {2025},
author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X},
title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.},
journal = {International journal of biological macromolecules},
volume = {306},
number = {Pt 4},
pages = {141714},
doi = {10.1016/j.ijbiomac.2025.141714},
pmid = {40043973},
issn = {1879-0003},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Fermentation ; Fatty Acids, Volatile/metabolism ; *Auricularia/chemistry ; Feces/microbiology ; Prebiotics ; *Polysaccharides/pharmacology/metabolism ; *Fungal Polysaccharides/pharmacology/metabolism ; Bacteria/metabolism/genetics ; Metabolomics ; },
abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Fermentation
Fatty Acids, Volatile/metabolism
*Auricularia/chemistry
Feces/microbiology
Prebiotics
*Polysaccharides/pharmacology/metabolism
*Fungal Polysaccharides/pharmacology/metabolism
Bacteria/metabolism/genetics
Metabolomics

@article {pmid39961944,
year = {2025},
author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A},
title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.},
journal = {Applied biochemistry and biotechnology},
volume = {197},
number = {5},
pages = {3503-3520},
pmid = {39961944},
issn = {1559-0291},
support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Composting ; *Metagenomics ; *Bacteria/genetics ; *Food ; *Microbiota ; *Metagenome ; *Soil Microbiology ; Food Loss and Waste ; },
abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.},
}

*Composting
*Metagenomics
*Bacteria/genetics
*Food
*Microbiota
*Metagenome
*Soil Microbiology
Food Loss and Waste

@article {pmid39887373,
year = {2025},
author = {Byrd, DA and Damerell, V and Gomez Morales, MF and Hogue, SR and Lin, T and Ose, J and Himbert, C and Ilozumba, MN and Kahlert, C and Shibata, D and Toriola, AT and Li, CI and Figueiredo, J and Stephens, WZ and Warby, CA and Hardikar, S and Siegel, EM and Round, J and Ulrich, CM and Gigic, B},
title = {The gut microbiome is associated with disease-free survival in stage I-III colorectal cancer patients.},
journal = {International journal of cancer},
volume = {157},
number = {1},
pages = {64-73},
doi = {10.1002/ijc.35342},
pmid = {39887373},
issn = {1097-0215},
support = {01KD2101D//German Federal Ministry of Education and Research/ ; R01 AG083580/AG/NIA NIH HHS/United States ; //Stiftung LebensBlicke/ ; //ERA-NET on Translational Cancer Research (TRANSCAN)/ ; //Rahel Goitein-Straus-Program/ ; 01KT1503//German Federal Ministry of Education and Research/ ; //Matthias-Lackas Foundations/ ; U01 CA206110/NH/NIH HHS/United States ; //Heidelberger Stiftung Chirurgie, Heidelberg University Hospital/ ; R01 CA189184/NH/NIH HHS/United States ; //Medizinische Fakultät Heidelberg, Universität Heidelberg/ ; U01 CA206110/CA/NCI NIH HHS/United States ; R01 CA189184/NH/NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/pathology/mortality ; Female ; Male ; Middle Aged ; Aged ; Feces/microbiology ; Disease-Free Survival ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Neoplasm Staging ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Colorectal cancer (CRC) is the second overall leading cause of cancer death in the United States, with recurrence being a frequent cause of mortality. Approaches to improve disease-free survival (DFS) are urgently needed. The gut microbiome, reflected in fecal samples, is likely mechanistically linked to CRC progression and may serve as a non-invasive biomarker. Accordingly, we leveraged baseline fecal samples from N = 166 stage I-III CRC patients in the ColoCare Study, a prospective cohort of newly diagnosed CRC patients. We sequenced the V3 and V4 regions of the 16S rRNA gene to characterize fecal bacteria. We calculated estimates of alpha diversity, beta diversity, and a priori- and exploratory-selected bacterial presence/absence and relative abundance. Associations of microbial metrics with DFS were estimated using multivariable Cox proportional hazards models. We found that alpha diversity was strongly associated with improved DFS, most strongly among rectal cancer patients (Shannon HRrectum = 0.40 95% CI = 0.19, 0.87; p = .02). Overall microbiome composition differences (beta diversity), as characterized by principal coordinate axes, were statistically significantly associated with DFS. Peptostreptococcus was statistically significantly associated with worse DFS (HR = 1.62, 95% CI = 1.13, 2.31; p = .01 per 1-SD) and Order Clostridiales was associated with improved DFS (HR = 0.62, 95% CI = 0.43-0.88; p = .01 per 1-SD). In exploratory analyses, Coprococcus and Roseburia were strongly associated with improved DFS. Overall, higher bacterial diversity and multiple bacteria were strongly associated with DFS. Metagenomic sequencing to elucidate species, gene, and functional level details among larger, diverse patient populations are critically needed to support the microbiome as a biomarker of CRC outcomes.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/pathology/mortality
Female
Male
Middle Aged
Aged
Feces/microbiology
Disease-Free Survival
RNA, Ribosomal, 16S/genetics
Prospective Studies
Neoplasm Staging
Bacteria/genetics/classification/isolation & purification

@article {pmid40325116,
year = {2025},
author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S},
title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15683},
pmid = {40325116},
issn = {2045-2322},
support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation & purification/genetics ; },
abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.},
}

Humans
*Lung Neoplasms/microbiology/pathology
Male
Female
Risk Factors
*Microbiota/genetics
Middle Aged
Aged
Lung/microbiology/pathology
High-Throughput Nucleotide Sequencing
Adult
Shewanella/isolation & purification/genetics

@article {pmid40323477,
year = {2025},
author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG},
title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {6},
pages = {195},
pmid = {40323477},
issn = {1559-131X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; },
abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.},
}

Humans
*Dysbiosis/microbiology
*Mycobiome
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Inflammation/microbiology
*Gastrointestinal Neoplasms/microbiology
Fungi/pathogenicity
Animals

@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}

*Machine Learning
*Microbiota
Humans
Spectrometry, Fluorescence/methods
*Bacteria/isolation & purification/genetics

@article {pmid38593566,
year = {2024},
author = {Pelpolage, SW and Kobayashi, H and Fukuma, N and Hoshizawa, M and Hamamoto, T and Han, KH and Fukushima, M},
title = {Temporal changes in the fermentation characteristics, bacterial community structure and the functionality of the predicted metagenome of a batch fermenter medium containing the upper gastrointestinal enzyme resistant fraction of white sorghum (Sorghum bicolor L. Moench).},
journal = {Food chemistry},
volume = {448},
number = {},
pages = {139102},
doi = {10.1016/j.foodchem.2024.139102},
pmid = {38593566},
issn = {1873-7072},
mesh = {*Sorghum/metabolism/chemistry/microbiology ; Fermentation ; Animals ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Swine ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism/enzymology ; Metagenome ; Digestion ; Starch/metabolism ; },
abstract = {Sorghum is a potential prebiotic ascribed to the high native resistant starch (RS) content. Our previous studies on raw sorghum have revealed prominent amino acid fermentation despite the high RS content. Interestingly, autoclaved-freeze-dried sorghum fed rats exhibited beneficial microbial and biochemical profiles. Having a keen interest to reciprocally scrutinize the underlying mechanisms behind these contrasting outcomes, we used an in vitro porcine batch fermentation model. The fermentable substrates in raw and autoclaved-freeze-dried (three cycles) sorghum (AC) after in vitro gastrointestinal digestion fostered similar bacterial community structures, yet with significant differences in the characteristic amylolytic microbial taxa abundance and their temporal variation. Further, significant differences in the concentration of organic acids in raw and AC manifested the differences in the predicted abundance of the underlying pathways of carbohydrate and organic acid metabolism. Thus, this study highlights the propensity of the heat-moisture treatment of sorghum in modifying the fermentability of its RS.},
}

*Sorghum/metabolism/chemistry/microbiology
Fermentation
Animals
*Bacteria/genetics/metabolism/classification/isolation & purification
Swine
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology/metabolism/enzymology
Metagenome
Digestion
Starch/metabolism

@article {pmid38470044,
year = {2024},
author = {Liu, D and Xie, L-S and Lian, S and Li, K and Yang, Y and Wang, W-Z and Hu, S and Liu, S-J and Liu, C and He, Z},
title = {Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil.},
journal = {mSphere},
volume = {9},
number = {4},
pages = {e0081623},
pmid = {38470044},
issn = {2379-5042},
support = {2022YFA1304103//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Humans ; *Fluorouracil/metabolism ; *Butyrates/metabolism ; Metagenomics ; Gastrointestinal Microbiome ; *Clostridiales/metabolism/genetics ; Genome, Bacterial ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; Phylogeny ; },
abstract = {UNLABELLED: Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications.

IMPORTANCE: This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.},
}

Humans
*Fluorouracil/metabolism
*Butyrates/metabolism
Metagenomics
Gastrointestinal Microbiome
*Clostridiales/metabolism/genetics
Genome, Bacterial
Colorectal Neoplasms/microbiology
Inflammatory Bowel Diseases/microbiology
Phylogeny

@article {pmid40322835,
year = {2025},
author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C},
title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {5},
pages = {e70082},
doi = {10.1111/aji.70082},
pmid = {40322835},
issn = {1600-0897},
support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; },
abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.

METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.

RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-κB, MMP3, IκBα, IL-1β, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.

CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.},
}

Animals
Female
*Moxibustion/methods
*Gastrointestinal Microbiome/immunology
Rats
*Th17 Cells/immunology
*Interleukin-17/metabolism
*Primary Ovarian Insufficiency/therapy/immunology/chemically induced
Rats, Sprague-Dawley
*Ovary/physiology
Signal Transduction
Disease Models, Animal

@article {pmid40321823,
year = {2025},
author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A},
title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19305},
pmid = {40321823},
issn = {2167-8359},
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Islands ; *Fungi/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Ecosystem ; *Microbiota ; },
abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.},
}

Brazil
*Soil Microbiology
*Biodiversity
*Bacteria/genetics/classification/isolation & purification
Islands
*Fungi/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Ecosystem
*Microbiota

@article {pmid40320520,
year = {2025},
author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J},
title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {111},
pmid = {40320520},
issn = {2049-2618},
support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; },
mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Droughts ; },
abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.},
}

*Microbiota/physiology
*Stress, Physiological
*Plants/microbiology
*Bacteria/classification/genetics/isolation & purification
Soil Microbiology
Droughts

@article {pmid40254113,
year = {2025},
author = {Bartáková, V and Bryjová, A and Polačik, M and Alila, DO and Nagy, B and Watters, B and Bellstedt, D and Blažek, R and Žák, J and Reichard, M},
title = {Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108357},
doi = {10.1016/j.ympev.2025.108357},
pmid = {40254113},
issn = {1095-9513},
mesh = {Animals ; Tanzania ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Genetics, Population ; Genetic Variation ; Sequence Analysis, DNA ; Metagenomics ; Killifishes ; },
abstract = {Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.},
}

Animals
Tanzania
*Phylogeny
Polymorphism, Single Nucleotide
*Genetics, Population
Genetic Variation
Sequence Analysis, DNA
Metagenomics
Killifishes

@article {pmid40175554,
year = {2025},
author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ},
title = {Bifidobacteria support optimal infant vaccine responses.},
journal = {Nature},
volume = {641},
number = {8062},
pages = {456-464},
pmid = {40175554},
issn = {1476-4687},
mesh = {*Bifidobacterium/immunology/physiology/drug effects/isolation & purification ; Mice ; Infant ; Animals ; Humans ; Female ; *Pneumococcal Vaccines/immunology ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Feces/microbiology ; Male ; Haemophilus Vaccines/immunology ; *Immunogenicity, Vaccine/immunology/drug effects ; Gastrointestinal Microbiome/drug effects/immunology ; Germ-Free Life ; Prospective Studies ; Probiotics/administration & dosage ; Vaccines, Conjugate/immunology ; Vaccination ; Antibodies, Bacterial/immunology ; },
abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.},
}

*Bifidobacterium/immunology/physiology/drug effects/isolation & purification
Mice
Infant
Animals
Humans
Female
*Pneumococcal Vaccines/immunology
Infant, Newborn
*Anti-Bacterial Agents/adverse effects/pharmacology
Feces/microbiology
Male
Haemophilus Vaccines/immunology
*Immunogenicity, Vaccine/immunology/drug effects
Gastrointestinal Microbiome/drug effects/immunology
Germ-Free Life
Prospective Studies
Probiotics/administration & dosage
Vaccines, Conjugate/immunology
Vaccination
Antibodies, Bacterial/immunology

@article {pmid39978335,
year = {2025},
author = {Wang, Z and Tian, L and Jiang, Y and Ning, L and Zhu, X and Chen, X and Xuan, B and Zhou, Y and Ding, J and Ma, Y and Zhao, Y and Huang, X and Hu, M and Fang, JY and Shen, N and Cao, Z and Chen, H and Wang, X and Hong, J},
title = {Synergistic role of gut-microbial L-ornithine in enhancing ustekinumab efficacy for Crohn's disease.},
journal = {Cell metabolism},
volume = {37},
number = {5},
pages = {1089-1102.e7},
doi = {10.1016/j.cmet.2025.01.007},
pmid = {39978335},
issn = {1932-7420},
mesh = {*Crohn Disease/drug therapy/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Ustekinumab/therapeutic use/pharmacology ; Male ; Female ; *Ornithine/metabolism/pharmacology ; Adult ; Animals ; Mice ; Th17 Cells/immunology/metabolism/drug effects ; Middle Aged ; Faecalibacterium prausnitzii/metabolism ; Signal Transduction/drug effects ; Treatment Outcome ; Feces/microbiology ; Receptors, Interleukin/metabolism ; },
abstract = {The role of the intestinal microbiome in Crohn's disease (CD) treatment remains poorly understood. This study investigates microbe-host interactions in CD patients undergoing ustekinumab (UST) therapy. Fecal metagenome, metabolome, and host transcriptome data from 85 CD patients were analyzed using multi-omics integration and mediation analysis. Our findings reveal significant microbiome-metabolite-host interactions. Specifically, Faecalibacterium prausnitzii was linked to altered L-ornithine biosynthesis, resulting in higher L-ornithine levels in patients before UST therapy. In vivo and in vitro studies demonstrated that microbiome-derived L-ornithine enhances UST treatment sensitivity in CD by disrupting the host IL-23 receptor signaling and inhibiting Th17 cell stabilization through the IL-12RB1/TYK2/STAT3 axis. L-ornithine significantly enhances the therapeutic efficacy of UST in CD patients, as demonstrated in a prospective clinical trial. These findings suggest that targeting specific microbe-host metabolic pathways may improve the efficacy of inflammatory bowel disease (IBD) treatments.},
}

*Crohn Disease/drug therapy/microbiology/metabolism
Humans
*Gastrointestinal Microbiome/drug effects
*Ustekinumab/therapeutic use/pharmacology
Male
Female
*Ornithine/metabolism/pharmacology
Adult
Animals
Mice
Th17 Cells/immunology/metabolism/drug effects
Middle Aged
Faecalibacterium prausnitzii/metabolism
Signal Transduction/drug effects
Treatment Outcome
Feces/microbiology
Receptors, Interleukin/metabolism

@article {pmid39950813,
year = {2025},
author = {Seguel Suazo, K and Nierychlo, M and Kondrotaite, Z and Petriglieri, F and Peces, M and Singleton, C and Dries, J and Nielsen, PH},
title = {Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {3},
pages = {e0148524},
pmid = {39950813},
issn = {1098-5336},
support = {13351//Villum Fonden (Villum Foundation)/ ; },
mesh = {*Wastewater/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/analysis ; *Biodiversity ; Sewage/microbiology ; },
abstract = {Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.},
}

*Wastewater/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics/analysis
*Biodiversity
Sewage/microbiology

@article {pmid40316630,
year = {2025},
author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD},
title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15356},
pmid = {40316630},
issn = {2045-2322},
support = {Small grant//Universidad del Rosario/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; },
abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metagenomics/methods
Male
*Energy Metabolism
Adult
Athletes
Young Adult
*Sports
Feces/microbiology
Female
Lipidomics

@article {pmid40314681,
year = {2025},
author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q},
title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.},
journal = {The new microbiologica},
volume = {48},
number = {1},
pages = {46-59},
pmid = {40314681},
issn = {1121-7138},
mesh = {Humans ; *Microbiota ; *Biomedical Research ; Bibliometrics ; Gastrointestinal Microbiome ; },
abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.},
}

Humans
*Microbiota
*Biomedical Research
Bibliometrics
Gastrointestinal Microbiome

@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}

@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}

Humans
*Peri-Implantitis/microbiology
*Saliva/microbiology
Pilot Projects
Cross-Sectional Studies
*Microbiota
*Dental Implants/microbiology
Male
Female
Biofilms/growth & development
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*Urinary Bladder Neoplasms/microbiology/urine
*DNA, Bacterial/isolation & purification/urine
Male
Female
Middle Aged
*Urine/microbiology
Aged
RNA, Ribosomal, 16S
Reproducibility of Results

@article {pmid40307949,
year = {2025},
author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ},
title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {108},
pmid = {40307949},
issn = {2049-2618},
support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.},
}

Humans
*Parkinson Disease/microbiology/complications
*Gastrointestinal Microbiome/genetics
Male
*REM Sleep Behavior Disorder/microbiology
Female
Aged
Middle Aged
Disease Progression
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40164832,
year = {2025},
author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA},
title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1240-1257},
pmid = {40164832},
issn = {2058-5276},
mesh = {Animals ; *Aging/genetics/physiology ; *Gastrointestinal Microbiome/genetics ; Mice ; *Caloric Restriction ; *Metagenome ; Humans ; Male ; Mice, Inbred C57BL ; Female ; Longevity ; },
abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.},
}

Animals
*Aging/genetics/physiology
*Gastrointestinal Microbiome/genetics
Mice
*Caloric Restriction
*Metagenome
Humans
Male
Mice, Inbred C57BL
Female
Longevity

@article {pmid40140705,
year = {2025},
author = {Garrido-Sanz, D and Keel, C},
title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1130-1144},
pmid = {40140705},
issn = {2058-5276},
mesh = {*Triticum/microbiology ; *Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; *Seeds/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Plant Roots/microbiology ; },
abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.},
}

*Triticum/microbiology
*Rhizosphere
Soil Microbiology
*Microbiota/genetics
*Seeds/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenomics
Plant Roots/microbiology

@article {pmid40307838,
year = {2025},
author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C},
title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {170},
pmid = {40307838},
issn = {1466-609X},
support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Female ; Intensive Care Units/organization & administration/statistics & numerical data ; Prospective Studies ; *Health Personnel/statistics & numerical data ; China ; Adult ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?

DESIGN: Prospective, multicentre, cross-sectional study.

SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.

PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.

MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.

RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change = 1.22, 95% CI: 1.12-1.34, p < 0.001). The β-diversity of ARG between the two groups differed significantly (p = 0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall = 0.96, p for nonlinear = 0.84).

CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.

TRIAL REGISTRATION: NCT06228248.},
}

Humans
Cross-Sectional Studies
Male
Female
Intensive Care Units/organization & administration/statistics & numerical data
Prospective Studies
*Health Personnel/statistics & numerical data
China
Adult
Middle Aged
*Drug Resistance, Microbial/genetics
Gastrointestinal Microbiome/genetics
Feces/microbiology

@article {pmid40307239,
year = {2025},
author = {Langwig, MV and Koester, F and Martin, C and Zhou, Z and Joye, SB and Reysenbach, AL and Anantharaman, K},
title = {Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4076},
pmid = {40307239},
issn = {2041-1723},
support = {DBI-2047598//National Science Foundation (NSF)/ ; OCE-2049478//National Science Foundation (NSF)/ ; },
mesh = {*Hydrothermal Vents/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; *Ecosystem ; Metagenome ; Genome, Viral ; Pacific Ocean ; Bacteriophages/genetics/classification ; Phylogeny ; Seawater/virology ; Gammaproteobacteria/virology ; Microbiota ; Virome ; },
abstract = {Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.},
}

*Hydrothermal Vents/virology/microbiology
*Viruses/genetics/classification/isolation & purification
*Ecosystem
Metagenome
Genome, Viral
Pacific Ocean
Bacteriophages/genetics/classification
Phylogeny
Seawater/virology
Gammaproteobacteria/virology
Microbiota
Virome

@article {pmid40307209,
year = {2025},
author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B},
title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4048},
pmid = {40307209},
issn = {2041-1723},
support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; },
abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.},
}

*Rhizosphere
*Arsenic/metabolism
Oxidation-Reduction
*Oryza/microbiology/virology/metabolism
Soil Microbiology
*Lysogeny/genetics
Microbiota/genetics
Gene Transfer, Horizontal
Metagenome
Plant Roots/microbiology/virology
Oxidoreductases/genetics/metabolism
Metabolic Reprogramming

@article {pmid40253770,
year = {2025},
author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J},
title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.},
journal = {International immunopharmacology},
volume = {156},
number = {},
pages = {114645},
doi = {10.1016/j.intimp.2025.114645},
pmid = {40253770},
issn = {1878-1705},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Rats ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; *Diabetes Mellitus, Experimental/drug therapy/metabolism ; *Hypoglycemic Agents/pharmacology/therapeutic use ; Bile/metabolism ; Diet, High-Fat ; Glucagon-Like Peptide 1/metabolism ; Insulin Resistance ; Blood Glucose/metabolism ; Coptis chinensis ; },
abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.

PURPOSE: This study aims to investigate the effects of BPRC on the gut microbiota and its metabolite SCFAs in T2DM rats.

METHODS: T2DM rat model was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), followed by a 4-week treatment with BPRC to observe its therapeutic effects. The impact of BPRC on the gut microbiota was studied through metagenomic sequencing. Quantitative analysis of SCFAs was conducted using GC-MS. Western blot and quantitative real-time PCR (qRT-PCR) were conducted to investigate the potential mechanisms of BPRC.

RESULTS: BPRC significantly improved insulin resistance in T2DM rats, downregulated levels of pancreatic cell apoptosis factors, and upregulated the abundance of Bacteroides uniformis, Bacteroides sp A1C1, Anaerostipes caccae, Alistipes finegoldii and Blautia sp.N6H1-15 in T2DM rats. Additionally, BPRC increased the levels of seven SCFAs in the intestines of T2DM rats. It activated intestinal TGR5, GPR41, GPR43, and GPR109a receptors, collectively upregulating GLP-1 protein expression, and exerted therapeutic effects on T2DM.

CONCLUSION: The results indicate that the synergistic mechanism of BPRC in treating T2DM is associated with modulating the gut microbiota, increasing SCFAs content in the intestines, and regulating intestinal GLP-1 production.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology
Male
*Drugs, Chinese Herbal/therapeutic use/pharmacology
Rats
*Fatty Acids, Volatile/metabolism
Rats, Sprague-Dawley
*Diabetes Mellitus, Experimental/drug therapy/metabolism
*Hypoglycemic Agents/pharmacology/therapeutic use
Bile/metabolism
Diet, High-Fat
Glucagon-Like Peptide 1/metabolism
Insulin Resistance
Blood Glucose/metabolism
Coptis chinensis

@article {pmid40058443,
year = {2025},
author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D},
title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.},
journal = {International journal of biological macromolecules},
volume = {307},
number = {Pt 1},
pages = {141858},
doi = {10.1016/j.ijbiomac.2025.141858},
pmid = {40058443},
issn = {1879-0003},
mesh = {Animals ; *Polysaccharides/pharmacology/chemistry ; *Osteoblasts/drug effects/metabolism ; *Osteomyelitis/drug therapy/metabolism/pathology ; Rats ; *MAP Kinase Signaling System/drug effects ; *Receptors, G-Protein-Coupled/metabolism ; Male ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Bone Regeneration/drug effects ; Disease Models, Animal ; },
abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.},
}

Animals
*Polysaccharides/pharmacology/chemistry
*Osteoblasts/drug effects/metabolism
*Osteomyelitis/drug therapy/metabolism/pathology
Rats
*MAP Kinase Signaling System/drug effects
*Receptors, G-Protein-Coupled/metabolism
Male
Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Bone Regeneration/drug effects
Disease Models, Animal

@article {pmid40035787,
year = {2025},
author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG},
title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {49},
number = {4},
pages = {451-459},
doi = {10.1002/jpen.2742},
pmid = {40035787},
issn = {1941-2444},
support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; },
mesh = {Humans ; Longitudinal Studies ; Male ; Female ; *Parenteral Nutrition ; *Gastrointestinal Microbiome ; Infant ; *Intestinal Failure/therapy/microbiology ; Child, Preschool ; Feces/microbiology ; *Weaning ; *Metabolomics ; Biomarkers/blood ; Cohort Studies ; Child ; Bacteria/classification/genetics ; Multiomics ; },
abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.

METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for ≤1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.

RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.

CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.},
}

Humans
Longitudinal Studies
Male
Female
*Parenteral Nutrition
*Gastrointestinal Microbiome
Infant
*Intestinal Failure/therapy/microbiology
Child, Preschool
Feces/microbiology
*Weaning
*Metabolomics
Biomarkers/blood
Cohort Studies
Child
Bacteria/classification/genetics
Multiomics

@article {pmid39930064,
year = {2025},
author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H},
title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {210},
pmid = {39930064},
issn = {2399-3642},
mesh = {*Museums ; *Metagenomics/methods ; *Genomics/methods ; Animals ; *DNA/genetics ; Archaeology ; Microbiota ; Greenland ; DNA, Ancient/analysis ; *Specimen Handling ; Bone and Bones/microbiology ; DNA Damage ; Fossils ; },
abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.},
}

*Museums
*Metagenomics/methods
*Genomics/methods
Animals
*DNA/genetics
Archaeology
Microbiota
Greenland
DNA, Ancient/analysis
*Specimen Handling
Bone and Bones/microbiology
DNA Damage
Fossils

@article {pmid38079031,
year = {2025},
author = {He, F and Jin, X and Sun, K and Zhao, L and Yang, W and Zhang, X and Dong, X and Zhao, Y and Pan, L and Bao, N and Sun, H},
title = {Bacillus subtilis JATP-3 Improves Nitrogen Metabolism by Regulating Intestinal Flora and AKG in Weaned Piglets.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {3},
pages = {1265-1276},
pmid = {38079031},
issn = {1867-1314},
support = {20210101019JC//Natural Science Foundation of Jilin Province/ ; },
mesh = {Animals ; Swine/microbiology/metabolism ; *Nitrogen/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; *Bacillus subtilis/physiology ; Weaning ; Animal Feed/analysis ; Male ; },
abstract = {Recently, it has been reported that oral probiotics improve the apparent digestibility of nitrogen in weaned piglets; however, the underlying mechanism is unclear. A total of 12 crossbred piglets (Yorkshire × Landrace; 28 days old) were randomly divided into two groups. The control (Con) group was fed with a basic diet + Luria-Bertani (LB; sterile; 10 mL), whereas the subject (Sub) group was fed with a basic diet + B. subtilis JATP-3 (1 × 10[9] CFU/mL; 10 mL). The results showed that feeding B. subtilis JATP-3 increased the final body weight and nitrogen deposition rate of weaned piglets (P < 0.05); while the daily weight gain showed an upward trend (P < 0.1). The abundance of Pedicoccus, Collinella, Turiciator, Veillonella, Clostridium, and Escherichia were significantly increased in the jejunum (P < 0.05). The abundance of Olsenella and Pediococcus were significantly increased in the ileum (P < 0.05). The metabolomics analysis showed that the levels of l-lactic acid and Alpha-ketoglutaric acid (AKG) in portal vein plasma were significantly increased (P < 0.05). In addition, the content of AKG in muscle and liver increased significantly (P < 0.01). The metagenomics analysis showed that Veillonella encoded the functional genes of 2-oxoglutarate synthase and promoted AKG production. The protein expression of eIF4E-binding protein 1 (4EBP1) phosphorylated in the skeletal muscle increased (P < 0.05). In summary, B. subtilis JATP-3 promotes dietary nitrogen metabolism and skeletal muscle synthesis by modulating the intestinal microbiota and its metabolites, in which AKG may be one of the main mediators of the therapeutic effects of B. subtilis JATP-3.},
}

Animals
Swine/microbiology/metabolism
*Nitrogen/metabolism
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/pharmacology
*Bacillus subtilis/physiology
Weaning
Animal Feed/analysis
Male

@article {pmid38070037,
year = {2025},
author = {Aziz, K and Gilbert, JA and Zaidi, AH},
title = {Genomic and Phenotypic Insight into the Probiotic Potential of Lactic Acid Bacterial spp. Associated with the Human Gut Mucosa.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {3},
pages = {1236-1264},
pmid = {38070037},
issn = {1867-1314},
support = {SIG # S10 OD026929/NH/NIH HHS/United States ; IRSIP//Higher Education Commision, Pakistan/ ; SIG # S10 OD026929/NH/NIH HHS/United States ; PSDP "Development of National Probiotics Lab at NIBGE"//Ministry of Planning, Development & Special Initiatives, Government of Pakistan/ ; },
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; Genome, Bacterial ; *Intestinal Mucosa/microbiology ; *Lactobacillus/genetics/physiology ; *Enterococcus/genetics/physiology ; Phenotype ; },
abstract = {Commensal microbiome-based health support is gaining respect in the medical community and new human gut-associated Lactic Acid Bacteria (LAB) strains must be evaluated for their probiotic potential. Here we characterized the phenotype and genomes of human ileocecal mucosa-associated LAB strains using metagenomic sequencing and in vitro testing. The strains characterized belonged to the genus Enterococcus (Enterococcus lactis NPL1366, NPL1371, and Enterococcus mundtii NPL1379) and Lactobacillus (Lactobacillus paragasseri, NPL1369, NPL1370, and Lactiplantibacillus plantarum NPL1378). Genome annotation suggested bacterial adaptation to both human physiological and industrial manufacturing-related stressors. Genes for histidine kinases in enterococci and Na + /K + antiporters and F0F1 ATP synthases in Lactobacillus strains may support their tolerance to acid seen in vitro. The bile salt hydrolase (BSH) gene in Lp. plantarum and L. paragasseri may help explain their reported bile salt deconjugation and cholesterol-lowering behavior. Thioredoxin is the principal antioxidant system, and several oxidases and general stress-related proteins are found in lactobacilli, most notably in L. plantarum NPL1378. Multiple adhesion and biofilm-related genes were predicted in the LAB genomes. Adhesion and biofilm-related genes figured prominently in the genomes of enterococcal strains, especially E. lactis, corresponding to its biofilm formation capacity in vitro. Bacteriocin and secondary metabolite biosynthetic gene clusters in the sequenced genomes of E. lactis NPL1366 and Lp. plantarum NPL1378 may explain their in vitro pathogenic antagonism. Moreover, folate producing Lp. plantarum strain holds potential to be used in therapeutics or biofortification of food. All the strains were deemed safe through in vitro and in silico analysis. This basic genetic and phenotypic information supports their contention as probiotic adjuncts to conventional medical therapy.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome
Genome, Bacterial
*Intestinal Mucosa/microbiology
*Lactobacillus/genetics/physiology
*Enterococcus/genetics/physiology
Phenotype

@article {pmid40305569,
year = {2025},
author = {Hernandez-Valencia, JC and Gómez, GF and Correa, MM},
title = {Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320593},
pmid = {40305569},
issn = {1932-6203},
mesh = {Animals ; *Anopheles/virology ; Colombia ; *Virome/genetics ; *Metagenomics/methods ; *Mosquito Vectors/virology ; Phylogeny ; Malaria/transmission ; Metagenome ; },
abstract = {Anopheles darlingi is a main malaria vector in the neotropical region, but its viral component is not well studied, especially in the neotropics. This work aimed to analyze the virome in Anopheles darlingi from malaria endemic regions of Colombia. Specimens were collected from the Bajo Cauca, Chocoan Pacific and northwestern Amazonas regions and analyzed using an RNA-Seq approach. Results revealed a variety of RNA viral sequences with homology to those of Insect-Specific Viruses belonging to Rhabdoviridae, Partitiviridae, Metaviridae, Tymoviridae, Phasmaviridae, Totiviridae, Ortervirales and Riboviria. Despite geographical and ecological differences among regions, the An. darlingi viral composition remains consistent in different areas, with a core group of viral operational taxonomic units-vOTUs shared by the populations. Furthermore, diversity analysis uncovered greater dissimilarities in viral sequence among mosquitoes from geographically distant regions, particularly evident between populations located at both sides of the Andes Mountain range. This study provides the first characterization of the metavirome in An. darlingi from Colombia and lays the foundation for future research on the complex interactions among viruses, hosts, and microbiota; it also opens a new line of investigation on the viruses in Anopheles populations of Colombia.},
}

Animals
*Anopheles/virology
Colombia
*Virome/genetics
*Metagenomics/methods
*Mosquito Vectors/virology
Phylogeny
Malaria/transmission
Metagenome

@article {pmid40305442,
year = {2025},
author = {Cayrou, C and Silver, K and Owen, L and Dunlop, J and Laird, K},
title = {Domestic laundering of healthcare textiles: Disinfection efficacy and risks of antibiotic resistance transmission.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321467},
pmid = {40305442},
issn = {1932-6203},
mesh = {*Disinfection/methods ; *Textiles/microbiology ; Humans ; *Laundering/methods ; Microbial Sensitivity Tests ; Detergents/pharmacology ; *Cross Infection/prevention & control/microbiology ; *Drug Resistance, Microbial ; Staphylococcus aureus/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; United Kingdom ; Microbiota/drug effects ; Decontamination/methods ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Enterococcus faecium/drug effects ; },
abstract = {Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are a major public health concern, with the evidence base for the potential role of textiles as fomites in microbial transmission growing. In the UK, domestic laundering machines (DLMs) are commonly used to clean healthcare worker uniforms, raising concerns about their effectiveness in microbial decontamination and role in AMR development. This study aimed to evaluate DLMs' ability to decontaminate microorganisms and their potential impact on AMR. The performance of six DLMs was assessed using Enterococcus faecium bioindicators under various wash cycles and detergent conditions. Shotgun metagenomics was used to analyse the microbiome and resistome of DLMs. The minimum inhibitory concentrations of domestic detergents were determined for Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, and detergent tolerance and antibiotic cross-resistance were assessed. Results showed only 50% (3/6) of DLMs achieved sufficient decontamination (≥5 log10 CFU reduction) at 60°C during full-length cycles, with rapid cycles performing inconsistently. Microbiome analysis revealed the presence of potentially pathogenic bacteria (e.g., Mycobacterium sp. Pseudomonas sp. and Acinetobacter sp.) and antibiotic resistance genes, including efflux pumps and target modification genes. Detergent tolerance assays showed increased bacterial tolerance to detergents, with cross-resistance to antibiotics observed in S. aureus and K. pneumoniae, including carbapenem and β-lactam groups. Whole genome sequencing identified mutations in genes encoding efflux pumps in S. aureus (MrgA) and K. pneumoniae (AcrB) after detergent exposure, which could impact efflux pump function. Findings suggest domestic laundering of healthcare uniforms may be insufficient for decontamination, posing risks for HAI transmission and AMR. Revising laundering guidelines to ensure effective DLM performance, detergent efficacy, and considering alternatives like onsite/industrial laundering are crucial to enhancing patient safety and controlling AMR in healthcare settings.},
}

*Disinfection/methods
*Textiles/microbiology
Humans
*Laundering/methods
Microbial Sensitivity Tests
Detergents/pharmacology
*Cross Infection/prevention & control/microbiology
*Drug Resistance, Microbial
Staphylococcus aureus/drug effects/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
United Kingdom
Microbiota/drug effects
Decontamination/methods
Klebsiella pneumoniae/drug effects
Pseudomonas aeruginosa/drug effects
Enterococcus faecium/drug effects

@article {pmid40304791,
year = {2025},
author = {Bu, Y and Zhang, X and Xiong, Z and Li, K and Zhang, S and Lin, M and Zhao, G and Zheng, N and Wang, J and Zhao, S},
title = {Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {107},
pmid = {40304791},
issn = {1432-0614},
support = {2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202308//the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Fermentation/drug effects ; *Isoflavones/pharmacology/administration & dosage/metabolism ; *Trifolium/chemistry ; Genistein/pharmacology/administration & dosage ; *Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; Female ; Ammonia/metabolism ; Urease/metabolism ; Urea/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Metagenomics ; },
abstract = {Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH3-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.},
}

Animals
Cattle
*Rumen/microbiology
*Fermentation/drug effects
*Isoflavones/pharmacology/administration & dosage/metabolism
*Trifolium/chemistry
Genistein/pharmacology/administration & dosage
*Bacteria/classification/genetics/drug effects/metabolism/isolation & purification
Female
Ammonia/metabolism
Urease/metabolism
Urea/metabolism
*Gastrointestinal Microbiome/drug effects
Animal Feed/analysis
Metagenomics

@article {pmid40258509,
year = {2025},
author = {Fang, C and Zhu, J and Xu, H and Qian, M and Jin, Y},
title = {Polystyrene microplastics and cypermethrin exposure interfered the complexity of antibiotic resistance genes and induced metabolic dysfunction in the gut of adult zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126288},
doi = {10.1016/j.envpol.2025.126288},
pmid = {40258509},
issn = {1873-6424},
mesh = {Animals ; *Zebrafish ; *Pyrethrins/toxicity ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polystyrenes/toxicity ; *Drug Resistance, Microbial/genetics ; Female ; },
abstract = {Environmental pollutants such as microplastics (MPs) and pesticides are becoming prevalent in aquatic ecosystems, posing risks to wildlife and human health. This study investigated the toxicological effects of polystyrene microplastics (PS-MPs) and cypermethrin (CYP) on adult female zebrafish (Danio rerio), focusing on intestinal microenvironment. Adsorption kinetics experimental results showed that PS-MPs can adsorb a certain amount of CYP on its surface, thereby forming a new type of composite pollutant. After exposure to red fluorescent PS-MPs for 4 days, it was found that the PS-MPs could enter the zebrafish and accumulate in the intestines. Five-month-old female zebrafish were exposed to PS-MPs, CYP, and a mixture of both for 21 days. After exposure, feces were collected and analyzed using metagenomic sequencing to determine microbial composition and functional changes. Metagenomic sequencing of naturally excreted feces showed that co-exposure synergistically reduced α-diversity and shifted community structure, with marked losses of beneficial Fusobacteriota, Firmicutes and Cetobacterium somerae and enrichment of pathogenic Preplasmiviricota. Functional annotation indicated that PS-MPs alone up-regulated glycoside hydrolases and glycosyl-transferases, whereas CYP and the co-exposure group suppressed a great number of the top 50 carbohydrate-active enzymes and decreased secondary metabolic pathways linked to amino-acid, lipid and carbohydrate metabolism pathways. Antibiotic-resistance gene (ARGs) profiling identified 57 ARG types (such as sul1, adeF, lnuC and mphA) after co-exposure. Finally, key genes related to amino acid metabolism, carbohydrate metabolism, and lipid metabolism in intestinal tissue were significantly altered. Collectively, our data demonstrated that PS-MPs and CYP exposure amplified gut dysbiosis, metabolic dysfunction and ARG complexity in zebrafish. Overall, the study highlighted the potential risks of combined environmental pollutants on intestinal microbiota, with implications for ecosystem health.},
}

Animals
*Zebrafish
*Pyrethrins/toxicity
*Microplastics/toxicity
*Water Pollutants, Chemical/toxicity
*Gastrointestinal Microbiome/drug effects
*Polystyrenes/toxicity
*Drug Resistance, Microbial/genetics
Female

@article {pmid40252750,
year = {2025},
author = {Yang, M and Peng, L and Mu, M and Yang, F and Li, Z and Han, B and Zhang, K},
title = {Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126277},
doi = {10.1016/j.envpol.2025.126277},
pmid = {40252750},
issn = {1873-6424},
mesh = {Animals ; *Oligochaeta ; *Manure/microbiology/analysis ; Metagenomics ; Livestock ; *Drug Resistance, Microbial/genetics ; Composting ; Anti-Bacterial Agents ; Metagenome ; Gastrointestinal Microbiome ; Bacteria/genetics ; },
abstract = {Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89 %) and Eisenia fetida (48.42 %), whereas Euryarchaeota (36.71 %) and Actinobacteria (39.42 %) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.},
}

Animals
*Oligochaeta
*Manure/microbiology/analysis
Metagenomics
Livestock
*Drug Resistance, Microbial/genetics
Composting
Anti-Bacterial Agents
Metagenome
Gastrointestinal Microbiome
Bacteria/genetics

@article {pmid40210162,
year = {2025},
author = {Gao, X and Yuan, S and Li, X and Xing, W},
title = {Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {374},
number = {},
pages = {126213},
doi = {10.1016/j.envpol.2025.126213},
pmid = {40210162},
issn = {1873-6424},
mesh = {*Geologic Sediments/microbiology ; *Nitrogen Cycle ; *Microplastics/toxicity ; *Water Pollutants, Chemical ; *Carbon Cycle ; Carbon/metabolism ; Nitrogen/metabolism ; Microbiota ; },
abstract = {Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5 % w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.},
}

*Geologic Sediments/microbiology
*Nitrogen Cycle
*Microplastics/toxicity
*Water Pollutants, Chemical
*Carbon Cycle
Carbon/metabolism
Nitrogen/metabolism
Microbiota

@article {pmid40081757,
year = {2025},
author = {Armengaud, J},
title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.},
journal = {Journal of proteomics},
volume = {316},
number = {},
pages = {105430},
doi = {10.1016/j.jprot.2025.105430},
pmid = {40081757},
issn = {1876-7737},
mesh = {Humans ; *Proteomics/methods ; *Microbiota/physiology ; Metabolomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome/physiology ; },
abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.},
}

Humans
*Proteomics/methods
*Microbiota/physiology
Metabolomics/methods
*Metagenomics/methods
*Gastrointestinal Microbiome/physiology

@article {pmid39643486,
year = {2025},
author = {Reyes-Sosa, MB and Valle-Gough, R and Ponce-Caballero, MDC and Arena-Ortiz, ML},
title = {Bacterial richness assessment in water and sediments in the northern coast of the Yucatan Peninsula.},
journal = {Revista Argentina de microbiologia},
volume = {57},
number = {2},
pages = {171-181},
doi = {10.1016/j.ram.2024.10.009},
pmid = {39643486},
issn = {0325-7541},
mesh = {*Geologic Sediments/microbiology ; *Water Microbiology ; Mexico ; *Bacteria/isolation & purification/classification/genetics ; *Biodiversity ; *Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Wetlands ; Microbiota ; },
abstract = {Given the importance of the coastal environments and the multiple ecological services that they provide, it is important to explore and understand the interactions that occur within them. The microbiome is a key factor for the understanding of the dynamics of these fragile sites. A metagenomic study based on the profiling of the 16S ribosomal gene was carried out in order to assess the bacterial diversity present in the northern coastal zone of the Yucatan Peninsula. The results showed that water and sediment samples share some similarities regarding the bacterial genera found, only differing in the quantitative part. Through a PCO (principal coordinates) analysis clear differences between sediment and water samples could be observed. The highest relative diversity was found in wetland and lagoon sediment samples, respectively. It was observed that 3-8% of the total sequence reads belonged to opportunistic genera such as: Vibrio in the sea samples and Capnocytophaga in the other environments. Salinity and pH were the factors which contributed the most to the differences among the communities in the various environments in the coastal zone. There is an important similarity in the sediments across the different environments within the studied coastal zone. The data presented herein contribute to setting a baseline for research in the coastal region of the Yucatan Peninsula.},
}

*Geologic Sediments/microbiology
*Water Microbiology
Mexico
*Bacteria/isolation & purification/classification/genetics
*Biodiversity
*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
Wetlands
Microbiota

@article {pmid40245686,
year = {2025},
author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, Á and Muñoz, S and García-Cañas, V},
title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {262},
number = {},
pages = {116896},
doi = {10.1016/j.jpba.2025.116896},
pmid = {40245686},
issn = {1873-264X},
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; *Methylamines/metabolism ; Metabolomics/methods ; *Fatty Acids, Volatile/metabolism ; Humans ; *Digestion/physiology ; *Nanopore Sequencing/methods ; Plant Extracts/pharmacology ; Models, Biological ; Fermentation ; Transcriptome ; },
abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.},
}

*Gastrointestinal Microbiome/physiology/drug effects
*Methylamines/metabolism
Metabolomics/methods
*Fatty Acids, Volatile/metabolism
Humans
*Digestion/physiology
*Nanopore Sequencing/methods
Plant Extracts/pharmacology
Models, Biological
Fermentation
Transcriptome

@article {pmid40210439,
year = {2025},
author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS},
title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.},
journal = {Genome research},
volume = {35},
number = {5},
pages = {1247-1260},
pmid = {40210439},
issn = {1549-5469},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Genetic Variation ; *Bacteria/genetics/classification ; },
abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Metagenome
*Genetic Variation
*Bacteria/genetics/classification

@article {pmid40081368,
year = {2025},
author = {Dai, R and Zhang, J and Liu, F and Xu, H and Qian, JM and Cheskis, S and Liu, W and Wang, B and Zhu, H and Pronk, LJU and Medema, MH and de Jonge, R and Pieterse, CMJ and Levy, A and Schlaeppi, K and Bai, Y},
title = {Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns.},
journal = {Cell},
volume = {188},
number = {9},
pages = {2521-2539.e22},
doi = {10.1016/j.cell.2025.02.013},
pmid = {40081368},
issn = {1097-4172},
mesh = {*Plant Roots/microbiology/virology ; *Genome, Viral/genetics ; *Microbiota/genetics ; *Crops, Agricultural/microbiology/virology ; *Bacteria/genetics/classification ; Phylogeny ; *Genome, Bacterial/genetics ; Soil Microbiology ; Metagenomics ; Zea mays/microbiology/virology ; Oryza/microbiology/virology ; Metagenome ; Triticum/microbiology/virology ; },
abstract = {Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.},
}

*Plant Roots/microbiology/virology
*Genome, Viral/genetics
*Microbiota/genetics
*Crops, Agricultural/microbiology/virology
*Bacteria/genetics/classification
Phylogeny
*Genome, Bacterial/genetics
Soil Microbiology
Metagenomics
Zea mays/microbiology/virology
Oryza/microbiology/virology
Metagenome
Triticum/microbiology/virology

@article {pmid40068786,
year = {2025},
author = {Wang, L and Zhao, G and Guo, W and Li, Y and Chen, J and Niu, L},
title = {Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121363},
doi = {10.1016/j.envres.2025.121363},
pmid = {40068786},
issn = {1096-0953},
mesh = {*Estuaries ; *Sulfur/metabolism ; China ; Geologic Sediments/microbiology/chemistry ; Rivers/microbiology ; *Water Pollutants, Chemical/metabolism ; Microbiota ; *Tidal Waves ; Environmental Monitoring ; },
abstract = {Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.},
}

*Estuaries
*Sulfur/metabolism
China
Geologic Sediments/microbiology/chemistry
Rivers/microbiology
*Water Pollutants, Chemical/metabolism
Microbiota
*Tidal Waves
Environmental Monitoring

@article {pmid40049354,
year = {2025},
author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J},
title = {Metabolic and ecological responses of denitrifying consortia to different carbon source strategies under fluctuating C/N conditions.},
journal = {Environmental research},
volume = {274},
number = {},
pages = {121292},
doi = {10.1016/j.envres.2025.121292},
pmid = {40049354},
issn = {1096-0953},
mesh = {*Denitrification ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Microbial Consortia ; Wastewater/microbiology ; Bioreactors/microbiology ; Bacteria/metabolism ; Waste Disposal, Fluid/methods ; },
abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.},
}

*Denitrification
*Carbon/metabolism
*Nitrogen/metabolism
*Microbial Consortia
Wastewater/microbiology
Bioreactors/microbiology
Bacteria/metabolism
Waste Disposal, Fluid/methods

@article {pmid38960277,
year = {2025},
author = {Li, W and Wang, Y and Zhao, K and Xu, L and Shi, T and Ma, B and Lv, X},
title = {Host-virus coevolution drives soil microbial function succession along a millennium land reclamation chronosequence.},
journal = {Journal of advanced research},
volume = {71},
number = {},
pages = {297-306},
doi = {10.1016/j.jare.2024.06.022},
pmid = {38960277},
issn = {2090-1224},
mesh = {*Soil Microbiology ; Metagenome ; *Host Microbial Interactions/genetics ; Virome/genetics ; Gene Transfer, Horizontal ; *DNA Viruses/genetics ; Soil/chemistry ; },
abstract = {INTRODUCTION: Gene exchange between viruses and hosts plays an important role in driving virus-host coevolution, enabling adaptation of both viruses and hosts to environmental changes. However, the mechanisms and functional significance of virus-host gene exchanges over long-term scales remain largely unexplored.

OBJECTIVE: The present study aimed to gain insights into the role of viruses in virus-host interactions and coevolution by monitoring virome dynamics along a millennium-long land reclamation chronosequence.

METHODS: We collected 24 soil samples from 8 stages of a millennium-long land reclamation chronosequence, including non-reclamation, and reclamation periods of 10, 50, 100, 300, 500, 700, and 1000 years. We characterized their metagenomes, and identified DNA viruses within these metagenomes.

RESULTS: Our findings reveal a significant shift in viral community composition after 50 years of land reclamation, but soil viral diversity reached a stable phase approximately 300 years after the initial reclamation. Analysis of the virus-host network showed a scale-free degree distribution and a reduction in complexity over time, with generalist viruses emerging as key facilitators of horizontal gene transfer.

CONCLUSION: These findings highlight the integral role of viruses, especially generalist types, in mediating gene exchanges between viruses and hosts, thereby influencing the coevolutionary dynamics in soil ecosystems over significant timescales. This study offers novel insights into long-term virus-host interactions, showing how the virome responds to environmental changes, driving shifts in various microbial functions in reclaimed land.},
}

*Soil Microbiology
Metagenome
*Host Microbial Interactions/genetics
Virome/genetics
Gene Transfer, Horizontal
*DNA Viruses/genetics
Soil/chemistry

@article {pmid40302838,
year = {2025},
author = {Pallen, MJ and Ponsero, AJ and Telatin, A and Moss, CJ and Baker, D and Heavens, D and Davidson, GL},
title = {Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.},
journal = {Access microbiology},
volume = {7},
number = {4},
pages = {},
pmid = {40302838},
issn = {2516-8290},
abstract = {Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.},
}

@article {pmid40295121,
year = {2025},
author = {Scheffer, G and Rattray, J and Evans, P and Shi, W and Bhatnagar, S and Hubert, CRJ},
title = {Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {5},
pages = {},
doi = {10.1093/femsec/fiaf041},
pmid = {40295121},
issn = {1574-6941},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //University of Calgary/ ; },
mesh = {*Nitrates/metabolism ; *Ponds/microbiology/chemistry ; *Oil and Gas Fields/microbiology ; Sulfates/metabolism ; *Bacteria/metabolism/genetics/classification ; *Water Microbiology ; Oxidation-Reduction ; Sulfides/metabolism ; Nitrites/metabolism ; Microbiota ; },
abstract = {Nitrate addition for mitigating sulfide production in oil field systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and reuse associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, and Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.},
}

*Nitrates/metabolism
*Ponds/microbiology/chemistry
*Oil and Gas Fields/microbiology
Sulfates/metabolism
*Bacteria/metabolism/genetics/classification
*Water Microbiology
Oxidation-Reduction
Sulfides/metabolism
Nitrites/metabolism
Microbiota

@article {pmid40209382,
year = {2025},
author = {Su, C and Kang, J and Liu, S and Li, C},
title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144192},
doi = {10.1016/j.foodchem.2025.144192},
pmid = {40209382},
issn = {1873-7072},
mesh = {*Morinda/microbiology/chemistry/growth & development/metabolism ; *Fruit/microbiology/chemistry/growth & development/metabolism ; *Fruit and Vegetable Juices/analysis/microbiology ; *Microbiota ; Fermentation ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Volatile Organic Compounds/metabolism/chemistry ; Taste ; },
abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.},
}

*Morinda/microbiology/chemistry/growth & development/metabolism
*Fruit/microbiology/chemistry/growth & development/metabolism
*Fruit and Vegetable Juices/analysis/microbiology
*Microbiota
Fermentation
*Flavoring Agents/metabolism/chemistry
*Bacteria/classification/genetics/isolation & purification/metabolism
Volatile Organic Compounds/metabolism/chemistry
Taste

@article {pmid40209373,
year = {2025},
author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J},
title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144178},
doi = {10.1016/j.foodchem.2025.144178},
pmid = {40209373},
issn = {1873-7072},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Stichopus/metabolism/microbiology/chemistry ; *Sea Cucumbers/metabolism/microbiology ; Polysaccharides/metabolism/analysis ; Collagen/metabolism ; },
abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.},
}

Animals
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/metabolism/isolation & purification
*Stichopus/metabolism/microbiology/chemistry
*Sea Cucumbers/metabolism/microbiology
Polysaccharides/metabolism/analysis
Collagen/metabolism

@article {pmid39919372,
year = {2025},
author = {Swain, S and Sahoo, P and Biswal, S and Sethy, K and Panda, AN and Sahoo, N},
title = {Fecal bacterial microbiota diversity characterized for dogs with atopic dermatitis: its alteration and clinical recovery after meat-exclusion diet.},
journal = {American journal of veterinary research},
volume = {86},
number = {5},
pages = {},
doi = {10.2460/ajvr.24.09.0274},
pmid = {39919372},
issn = {1943-5681},
mesh = {Animals ; *Dermatitis, Atopic/veterinary/microbiology/diet therapy ; Dogs ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; *Dog Diseases/microbiology/diet therapy ; Animal Feed/analysis ; Female ; Meat ; Male ; RNA, Ribosomal, 16S ; Bacteria/classification/isolation & purification ; India ; },
abstract = {OBJECTIVE: To achieve clinical recovery in canine atopic dermatitis affected pet dogs via alteration of the gut microbiome, following a meat and egg exclusion diet for 60 days.

METHODS: 24 atopic dermatitis-affected pet dogs, all fed poultry meat and egg, and another 48 apparently healthy controls fed both poultry meat and egg (n = 24) or vegetable diet (24) were included in the study. The study was undertaken in the Bhubaneswar Smart City, Odisha, India, from July to December 2023. Fecal samples were collected at 2 points for DNA analysis, ie, on day 0 and day 60 of the change from a meat/egg-based diet to a vegetable-based diet. Extracted DNA samples were pooled category-wise and subjected to the gut microbiome analysis in the Nanopore sequencer targeting the 16S rRNA gene. Burrows-Wheeler Transform, Ferragina-Manzini index, and Krona charts were used for taxonomical classification and visualization of relative abundances of bacterial species within the metagenome. Alpha- and beta-diversity analyses were performed.

RESULTS: Atopic pets at day 0 showed elevation in the gut microbiome population with an adequate concentration of pathogens like Escherichia coli and Clostridiodes difficile with lower amounts of the beneficial bacteria like Lactobacillus sp, while the pets at 60 days after dietary intervention showed a significant decline in bacterial species like E coli and C difficile with higher amount of Lactobacillus sp. Both control groups showed variations of microbiome between them as well as from the atopic pets.

CONCLUSIONS: We found a close association of poultry meat/egg diet with gut microbiome population and atopic symptoms as well in dogs, and elimination of such diet could be helpful in clinical recovery.

CLINICAL RELEVANCE: Dietary intervention with the exclusion of potential allergens from poultry meat and egg sources can be an effective approach for the management of canine atopic dermatitis.},
}

Animals
*Dermatitis, Atopic/veterinary/microbiology/diet therapy
Dogs
*Feces/microbiology
*Gastrointestinal Microbiome
*Diet/veterinary
*Dog Diseases/microbiology/diet therapy
Animal Feed/analysis
Female
Meat
Male
RNA, Ribosomal, 16S
Bacteria/classification/isolation & purification
India

@article {pmid39838455,
year = {2025},
author = {Liao, H and Li, J and Wang, YZ and Li, H and An, XL and Wang, T and Chang, RY and Zhu, YG and Su, JQ},
title = {Evolutionary diversification and succession of soil huge phages in glacier foreland.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {18},
pmid = {39838455},
issn = {2049-2618},
support = {4237070301//National Natural Science Foundation of China/ ; 42161134002//National Natural Science Foundation of China/ ; STEP, 2021QZKK0103//Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Bacteriophages/genetics/classification/isolation & purification ; *Soil Microbiology ; Phylogeny ; *Ice Cover/virology/microbiology ; Metagenomics/methods ; Tibet ; Genome, Viral ; Biodiversity ; Evolution, Molecular ; Soil ; },
abstract = {BACKGROUND: Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.

RESULTS: Here, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.

CONCLUSIONS: Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. Video Abstract.},
}

*Bacteriophages/genetics/classification/isolation & purification
*Soil Microbiology
Phylogeny
*Ice Cover/virology/microbiology
Metagenomics/methods
Tibet
Genome, Viral
Biodiversity
Evolution, Molecular
Soil

@article {pmid40301729,
year = {2025},
author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S},
title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {39},
pmid = {40301729},
issn = {2730-7182},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.

RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200 m, with a slight increase observed above 1400 m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.

CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome
India
RNA, Ribosomal, 16S/genetics/analysis
*Altitude
*Bacteria/classification/genetics/isolation & purification

@article {pmid40301728,
year = {2025},
author = {Munoz Briones, J and Brubaker, DK},
title = {A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {115},
pmid = {40301728},
issn = {1471-2105},
support = {2120200//Directorate for Biological Sciences/ ; R01HD110367//National Institute of Child Health and Human Development/ ; },
mesh = {Humans ; *Microbiota ; *Metabolomics/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; *Computational Biology/methods ; Principal Component Analysis ; Crohn Disease/microbiology ; Multiomics ; },
abstract = {BACKGROUND: The number and size of multi-omics datasets with paired measurements of the host and microbiome is rapidly increasing with the advance of sequencing technologies. As it becomes routine to generate these datasets, computational methods to aid in their interpretation become increasingly important. Here, we present a framework for integration of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE integrates multi-omics data using single-omic latent variables (LV) organized in a structured meta-model to determine the combinations of features most predictive of a phenotype or condition.

RESULTS: We developed a supervised version of LIVE leveraging sparse Partial Least Squares Discriminant Analysis (sPLS-DA) LVs, and an unsupervised version leveraging sparse Principal Component Analysis (sPCA) principal components which both can incorporate covariate awarness. LIVE performance was tested on publicly available metagenomic and metabolomics data set from Crohn's Disease (CD) and Ulcerative Colitis (UC) status patients in the PRISM and LLDeep cohorts, and benchmarked against existing gut microbiome multi-omics approaches and vaginal microbiome datasests, achieving consistent and comparable performances. In addition to these benchmarking efforts, we present a detailed analysis and interpretation of both versions of LIVE using the PRISM and LLDeep cohorts. LIVE reduced the number of feature interactions from the original datasets for CD and UC from millions to less than 20,000 while conditioning the disease-predictive power of gut microbes, metabolites, enzymes, on clinical variables.

CONCLUSIONS: LIVE makes a distinct, complementary contribution to current methods to integrate microbiome data and offers key advantages to existing approaches in the interpretable integration of multi-omics data with clinical variables to predict to disease outcomes and identify microbiome mechanisms of disease.},
}

Humans
*Microbiota
*Metabolomics/methods
Gastrointestinal Microbiome
Metagenomics/methods
*Computational Biology/methods
Principal Component Analysis
Crohn Disease/microbiology
Multiomics

@article {pmid40301726,
year = {2025},
author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J},
title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {258},
pmid = {40301726},
issn = {1471-2180},
support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; },
mesh = {Humans ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Culture Media/chemistry ; *Biodiversity ; *Bacteriological Techniques/methods ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.},
}

Humans
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification/growth & development
*Metagenomics/methods
*Gastrointestinal Microbiome
Culture Media/chemistry
*Biodiversity
*Bacteriological Techniques/methods
Sequence Analysis, DNA
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid40298543,
year = {2025},
author = {Bisaccia, M and Berini, F and Marinelli, F and Binda, E},
title = {Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298543},
issn = {2079-6382},
support = {PNRA16_00105//Italian Ministry of Education, University and Research/ ; CMPT228810//Consorzio Interuniversitario per le Biotecnologie & Italian Ministry of Education, University and Research/ ; IBFM NBFC CN00000033//National Biodiversity Future Center/ ; PNRA22_0000040//Italian Ministry of Education, University and Research/ ; },
abstract = {The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.},
}

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

*Metagenomics/methods
Computational Biology/methods
*Software
*Gene Expression Profiling/methods
*Microbiota
Data Collection
Quality Control
Workflow
RNA, Untranslated
Molecular Sequence Annotation
Rhizosphere
Automation

@article {pmid40250228,
year = {2025},
author = {Wang, H and Yang, Q and Wang, S},
title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179427},
doi = {10.1016/j.scitotenv.2025.179427},
pmid = {40250228},
issn = {1879-1026},
mesh = {*Triticum/growth & development ; *Soil Microbiology ; Soil/chemistry ; *Agriculture/methods ; Phosphorus/analysis ; Nitrogen/analysis ; Metagenomics ; Microbiota ; Carbon/analysis ; Nitrogen Cycle ; },
abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.},
}

*Triticum/growth & development
*Soil Microbiology
Soil/chemistry
*Agriculture/methods
Phosphorus/analysis
Nitrogen/analysis
Metagenomics
Microbiota
Carbon/analysis
Nitrogen Cycle

@article {pmid40098591,
year = {2025},
author = {Hernández-Trujillo, PN and Lopez-Barón, CA and Arévalo-Pinzón, G and Trujillo-Güiza, ML and González-Duque, MI and Flórez, AM and Franco, DC and Vanegas, J},
title = {Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach.},
journal = {HIV medicine},
volume = {26},
number = {5},
pages = {785-799},
doi = {10.1111/hiv.70014},
pmid = {40098591},
issn = {1468-1293},
support = {2022218//Universidad Antonio Nariño/ ; },
mesh = {Humans ; Male ; Adult ; *Homosexuality, Male ; Metagenomics ; *HIV Infections/microbiology ; *Anal Canal/microbiology ; Middle Aged ; *Rectum/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; },
abstract = {INTRODUCTION: The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.

MATERIALS AND METHODS: In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.

RESULTS: Initially, 90 samples were collected, with 20 discarded due to having less than 200 ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p = 0.45) and beta diversity (PERMANOVA R = -0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.

CONCLUSION: Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.},
}

Humans
Male
Adult
*Homosexuality, Male
Metagenomics
*HIV Infections/microbiology
*Anal Canal/microbiology
Middle Aged
*Rectum/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome

@article {pmid39823337,
year = {2025},
author = {Wu, D and Seshadri, R and Kyrpides, NC and Ivanova, NN},
title = {A metagenomic perspective on the microbial prokaryotic genome census.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2166},
pmid = {39823337},
issn = {2375-2548},
mesh = {*Metagenomics/methods ; Phylogeny ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Metagenome ; *Genome, Bacterial ; *Genome, Archaeal ; Humans ; Biodiversity ; },
abstract = {Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.},
}

*Metagenomics/methods
Phylogeny
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Metagenome
*Genome, Bacterial
*Genome, Archaeal
Humans
Biodiversity

@article {pmid40297591,
year = {2025},
author = {Pei, X and Liu, L and Han, Y},
title = {Advances in human microbiome and prostate cancer research.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576679},
pmid = {40297591},
issn = {1664-3224},
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology
Male
*Microbiota
*Gastrointestinal Microbiome
Tumor Microenvironment/immunology
Animals

@article {pmid40297587,
year = {2025},
author = {Dora, D and Revisnyei, P and Pasic, A and Galffy, G and Dulka, E and Mihucz, A and Roskó, B and Szincsak, S and Iliuk, A and Weiss, GJ and Lohinai, Z},
title = {Host and bacterial urine proteomics might predict treatment outcomes for immunotherapy in advanced non-small cell lung cancer patients.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1543817},
pmid = {40297587},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology ; Male ; Female ; *Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology ; Middle Aged ; *Proteomics/methods ; Aged ; Immunotherapy/methods ; Treatment Outcome ; *Proteome ; Biomarkers, Tumor/urine ; Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {INTRODUCTION: Urine samples are non-invasive approaches to study potential circulating biomarkers from the host organism. Specific proteins cross the bloodstream through the intestinal barrier and may also derive from gut microbiota. In this study, we aimed to evaluate the predictive role of the host and bacterial urine extracellular vesicle (EV) proteomes in patients with non-small cell lung cancer (NSCLC) treated with anti-PD1 immunotherapy.

METHODS: We analyzed the urine EV proteome of 33 advanced-stage NSCLC patients treated with anti-PD1 immunotherapy with LC-MS/MS, stratifying patients according to long (>6 months) and short (≤6 months) progression-free survival (PFS). Gut microbial communities on a subcohort of 23 patients were also analyzed with shotgun metagenomics. Internal validation was performed using the Random Forest (RF) machine learning (ML) algorithm. RF was validated with a non-linear Bayesian ML model. Gene enrichment, and pathway analysis of host urine proteins were analyzed using the Reactome and Gene Ontology databases.

RESULTS: We identified human (n=3513), bacterial (n=2647), fungal (n=19), and viral (n=4) proteins. 186 human proteins showed differential abundance (p<0.05) according to PFS groups, 101 being significantly more abundant in patients with short PFS and n=85 in patients with long PFS. We found several pathways that were significantly enriched in patients with short PFS (vs long PFS). Multivariate Cox regression showed that human urine proteins MPP5, IGKV6-21, NT5E, and KRT27 were strongly associated with long PFS, and LMAN2, NUTF2, NID1, TNC, IGF1, BCR, GPHN, and PPBP showed the strongest association with short PFS. We revealed that an increased bacterial/host protein ratio in the urine is more frequent in patients with long PFS. Increased abundance of E. coli and E. faecalis proteins in the urine positively correlates with their gut metagenomic abundance. RF ML model supported the reliability in predicting PFS for critical human urine proteins (AUC=0.89), accuracy (95%) and Bacterial proteins (AUC=0.74).

CONCLUSION: To our knowledge, this is the first study to depict the predictive role of the host and bacterial urine proteome in anti-PD1-treated advanced NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology
Male
Female
*Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology
Middle Aged
*Proteomics/methods
Aged
Immunotherapy/methods
Treatment Outcome
*Proteome
Biomarkers, Tumor/urine
Gastrointestinal Microbiome
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}

*Plant Leaves/metabolism/microbiology
*Bacteria/genetics/metabolism
*Fungi/genetics/metabolism
*Rivers/microbiology
Ecosystem
Alnus
Transcriptome
RNA, Ribosomal, 16S/genetics